The binding of peptide nucleic acids (PNAs), novel antisense agents, to their complementary oligonucleotide is characterized by capillary gel electrophoresis (CGE). The ability of CGE to resolve the free and bound species enables the measurement of relative binding kinetics and the stoichiometry of binding. The binding kinetics depend on the relative sequence orientation of the target oligonucleotides. The stoichiometry of binding is 1:1 for the PNA-oligodeoxynucleotide heteroduplex whereas the stoichiometry for the PNA-oligoribonucleotide is more complicated.